Files are Different after Uploading to an FTP Site

There are two common reasons why files will be different immediately after uploading them:

File Size No Longer Matches

Text files (HTML, source code, etc) can be stored in a slightly different format on FTP sites, and that can make the file sizes increase or decrease by a small percentage.
Beyond Compare's file viewers and rules-based comparison both handle these differences, but a size-only comparison can not.
Beyond Compare can't detect this directly, so to make the files match you'll need to use a rules-based comparison or turn off size comparisons and rely on the files' dates.

File Date/Timestamp No Longer Matches

Not all FTP sites support changing the date on uploaded files.
When this happens the file's date will instead be the time that you uploaded it.

To work around this in many cases:

BC version 3 or 4

Select Session | Session Settings and pick the Handling tab.

In the File Handling group, enable the Touch local files when copying to an FTP site option.

BC version 2

Select Session | Comparison Control and pick the Advanced tab.

In the Miscellaneous group, enable the Touch local files when copying to an FTP site option.

After you upload the file Beyond Compare will copy the date from the FTP site and update the local file, and the files will match next time you compare them.